PCR Amplification of DNA

The Biotechnology Education Company Revised and Updated PCR Amplification of DNA Storage: See Page 3 for specific storage instructions EXPERIMENT OBJECTIVE: The objective of this experiment is for students to gain hands-on experience of the principles and practice of Polymerase Chain Reaction (PCR). This experiment is designed for DNA staining with InstaStain Ethidium Bromide or alternatively, can be stained with InstaStain Blue. EDVOTEK, Inc. 1-800-EDVOTEK www.edvotek.com EVT.120706

2 xxx Table of Contents PCR Amplification of DNA Experiment Components 3 Experiment Requirements 4 Background Information 5 Experiment Procedures Experiment Overview and General Instructions 8 Laboratory Safety 9 Module I: PCR Reaction Option A: Using A Thermal Cycler 10 Option B: Using Three Waterbaths 12 Module II: Separation of PCR Reactions by Electrophoresis 14 Module III: Size Determination of PCR Amplified DNA Fragment 16 Study Questions 18 Instructor's Guidelines Notes to the Instructor 20 Pre-Lab Preparations 23 Experiment Results and Analysis 24 Study Questions and Answers 25 Appendices A PCR Experimental Success Guidelines 28 B Polymerase Chain Reaction Using Three Waterbaths 29 C Preparation and Handling of PCR Samples With Wax 30 D 0.8% Agarose Gel Preparation 31 E 0.8% Agarose Gels - Quantity Preparations 32 F Staining and Visualization of DNA with InstaStain Ethidium Bromide Cards 33 G InstaStain Blue: One Step Staining and Destaining 34 Material Safety Data Sheets 35 EVT.120706 EDVOTEK, The Biotechnology Education Company, InstaStain, and UltraSpec-Agarose are trademarks of EDVOTEK, Inc. EDVOTEK -

PCR Amplification of DNA Experiment Components 3 Experiment # contains reagents to perform ten sets of Polymerase Chain Reaction (PCR) reactions. Sample volumes are very small. For liquid samples, it is important to quick spin the tube contents in a microcentrifuge to obtain suffi cient volume for pipeting. Spin samples for 10-20 seconds at maximum speed. Storage A Tubes with PCR reaction pellets Room Temp. Each PCR reaction pellet contains dntp Mixture Taq DNA Polymerase Buffer Taq DNA Polymerase MgCl 2 B Primer Mix (two primers) -20 C Freezer C Standard DNA Markers -20 C Freezer D Enzyme Grade Ultrapure Water -20 C Freezer E DNA Template for Amplification -20 C Freezer Reagents & Supplies Store all components below at room temperature. All components are intended for educational research only. They are not to be used for diagnostic or drug purposes, nor administered to or consumed by humans or animals. UltraSpec-Agarose Electrophoresis Buffer (50x) 10x Gel Loading Solution InstaStain Ethidium Bromide InstaStain Blue Microcentrifuge Tubes PCR tubes Wax beads THIS EXPERIMENT DOES NOT CONTAIN HUMAN DNA. None of the experiment components are derived from human sources. EDVOTEK - The Biotechnology Education Company 1-800-EDVOTEK www.edvotek.com FAX: 202-370-1501 email: info@edvotek.com EVT.120706

4 xxx PCR Amplification of DNA Experiment Requirements *If you do not have a thermal cycler, PCR experiments can be conducted, with proper care, using three waterbaths. However, a thermal cycler assures a signifi cantly higher rate of success. For Experiment Option A: Thermal Cycler (Cat. #541 is recommended) For Experiment Option B: Three waterbaths* (94 C, 45 C, and 72 C) Other Requirements For Both Options A & B: Horizontal gel electrophoresis apparatus D.C. power supply Balance Microcentrifuge UV Transilluminator or UV Photodocumentation system UV safety goggles Automatic micropipets (5-50 µl & 0.5-10 µl) with tips Microwave, hot plate or burner Pipet pump 250 ml flasks or beakers Hot gloves Disposable vinyl or latex laboratory gloves Ice buckets and ice Distilled or deionized water Isopropanol EDVO-TECH SERVICE 1-800-EDVOTEK Mon - Fri (1-800-338-6835) 9 am - 6 pm ET Technical Service Department Mon - Fri 9:00 am to 6:00 pm ET FAX: 202-370-1501 Web: www.edvotek.com email: info@edvotek.com Please have the following information ready: Online Ordering now available Visit our web site for information about EDVOTEK s complete line of hands-on experiments for biotechnology and biology education. Experiment number and title Kit lot number on box or tube Literature version number (in lower right corner) Approximate purchase date EVT.120706 EDVOTEK -

PCR Amplification of DNA 5 Polymerase Chain Reaction The polymerase chain reaction (PCR) is a DNA amplification technique that has revolutionized almost all aspects of biological research. The PCR technique was invented in 1984 by Dr. Kary Mullis while at Cetus Corporation. Mullis was awarded a Nobel Prize for his work in 1994. PCR allows for the amplification of a small quantity of DNA over one million-fold. The enormous utility of PCR is based on its procedural simplicity and specificity. Since the first application of PCR to diagnose sickle cell anemia, a large number of procedures have been developed. PCR has made amplification of DNA an alternate approach to cloning experiments. PCR is also used extensively in forensics, paternity/kinship testing, and the identification of human remains. PCR amplification requires the use of a thermostable DNA polymerase. The most commonly used of these is Taq DNA polymerase, purified from a bacterium known as Thermus Aquaticus that inhabits hot springs. This enzyme remains stable at near-boiling temperatures. Also included in the PCR reaction are the four deoxynucleotides (datp, dctp, dgtp, and dttp) and two synthetic oligonucleotides, typically 15-30 base pairs in length, known as "primers". These components, together with the DNA to be amplified, are incubated in an appropriate buffer that contains Mg2+. The primers are designed and synthesized to correspond to the start and end of the DNA to be amplified, known as the "template" or "target". If the template DNA is prepared from biological tissue, freshly isolated DNA will give the best amplification results. DNA extracted from older specimens may be degraded and therefore less suitable for amplification. Background Information The PCR reaction mixture (which contains the Taq DNA polymerase, buffer, deoxynucleotides, primers, and template) is subjected to sequential heating/cooling cycles at three different temperatures. The three temperatures are the basis of the PCR process (Figure 1). In the first step, the template is heated to near boiling (92-96 C.) to denature or "melt" the DNA. This step, known as "denaturation" disrupts the hydrogen bonds between the two complementary DNA strands and causes their complete separation. In the second PCR step, the mixture is cooled to a temperature that is typically in the range of 45-65. In this step, known as "annealing", the primers, present in great excess to the template, bind to the separated DNA strands. In the third PCR step, known as "extension", the temperature is raised to an intermediate value, usually 72 C. At this temperature the Taq DNA polymerase is maximally active and adds nucleotides to the primers to complete the synthesis of the new complementary strands. The exact temperature and incubation time required for each step depends on several factors, including the length of the target DNA and GC content of the primer/template. In some cases, the annealing and extension steps may be combined resulting in a two step per PCR cycle. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

6 PCR Amplification of DNA Polymerase Chain Reaction Background Information The three PCR steps of denaturation, annealing, and extension constitute one "cycle" and result in a doubling of the template copies in the mixture. The process is typically repeated for 20-40 cycles. Theoretically, if the reaction is allowed to be repeated for (n) cycles, the number of copies of template DNA will be 2n following completion, as shown at the bottom of Figure 1. For example, one would anticipate one million-fold amplification after 20 cycles. In theory, this process could continue indefinitely. In practice, however, the amount of product reaches a maximum after about 40 cycles, due to the depletion of reaction components and loss of DNA polymerase activity. One common problem that occurs during PCR is unwanted amplification products. These are due to contamination of the sample or nonspecific annealing of the primers. To reduce contamination, autoclaved tubes, pipet tips, and sterile water should be used. Gloves should always be worn when performing PCR. To minimize unwanted PCR products due to nonspecific primer annealing, the primer concentration should be minimized, if possible. Another common technique is "hot start", in which the components of the PCR reaction are fully mixed only after the DNA is fully denatured above 94 C. Following PCR, the amplified product is processed, depending on the objective of the experiment. In most cases, the DNA is subjected to either agarose or polyacrylamide gel electrophoresis. In DNA fingerprinting, used in criminal forensics, PCR-amplified DNA from the crime scene is compared to amplified DNA from suspects. In cloning experiments, the amplified DNA is typically further purified and ligated into the desired vector. In DNA sequencing experiments, the amplified DNA (usually radioactively labeled) is run on a thin polyacrylamide gel sequencing gel. The gel is then placed on a piece of film, which is activated by the radioactive molecules and developed to create an image of the DNA fragments in the gel. Alternatively, one may avoid the use of radioactivity by subjecting the sequencing gel to silver staining, in which silver ions bind directly to the DNA fragments. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 7 Polymerase Chain Reaction Target Sequence = Separation of two DNA strands 3' 3' = Primer 1 Cycle 1 = Primer 2 3' 3' 3' 3' Denature 94 C Anneal 2 primers 40 C - 65 C The Experiment 3' 3' Extension 72 C Cycle 2 3' 3' 3' 3' 3' 3' Cycle 3 3' 3' 3' 3' 3' 3' 3' 3' Figure 1: The Polymerase Chain Reaction Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

8 PCR Amplification of DNA Experiment Overview and General Instructions BEFORE YOU START THE EXPERIMENT 1. Read all instructions before starting the experiment. The Experiment 2. If you will be conducting PCR using a thermal cycler without a heated lid, also read the Appendix entitled "Preparation and Handling PCR Samples with Wax ". 3. If you will be using three waterbaths to conduct PCR, read the two appendices entitled "Polymerase Chain Reaction Using Three Waterbaths" and "Handling samples with wax overlays". 4. Write a hypothesis that reflects the experiment and predict experimental outcomes. EXPERIMENT OBJECTIVE: The objective of this experiment is for students to gain hands-on experience of the principles and practice of Polymerase Chain Reaction (PCR). BRIEF DESCRIPTION OF EXPERIMENT: In this experiment, students will learn the basic concepts of PCR by observing the increased accumulation of product with increasing number of cycles. The experiment is divided into three modules: 1) setting up and running the PCR reaction; 2) gel electrophoresis to separate the reaction mixture; and 3) visualization of the DNA patterns and size determination of the amplified product by comparison to standard DNA markers. This experiment has three modules: I. PCR Reaction II. Separation of PCR Reactions by Electrophoresis III. Size Determination of PCR Amplified DNA Fragment GEL SPECIFICATIONS This experiment requires a gel with the following specifications: Recommended gel size 7 x 7 cm Number of sample wells required 6 Placement of well-former template first set of notches Gel concentration required 0.8% Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 9 Laboratory Safety 1. Gloves and goggles should be worn routinely as good laboratory practice. 2. Exercise extreme caution when working with equipment that is used in conjunction with the heating and/or melting of reagents. 3. DO NOT MOUTH PIPET REAGENTS - USE PIPET PUMPS. 4. Exercise caution when using any electrical equipment in the laboratory. Although electrical current from the power source is automatically disrupted when the cover is removed from the apparatus, first turn off the power, then unplug the power source before disconnecting the leads and removing the cover. The Experiment Turn off power and unplug the equipment when not in use. 5. EDVOTEK injection-molded electrophoresis units do not have glued junctions that can develop potential leaks. However, in the unlikely event that a leak develops in any electrophoresis apparatus you are using, IM- MEDIATELY SHUT OFF POWER. Do not use the apparatus. 6. Always wash hands thoroughly with soap and water after handling reagents or biological materials in the laboratory. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

10 PCR Amplification of DNA Module I - Option A: PCR Reaction Using a Thermal Cycler 1. Label three 0.5 ml tubes: "0" (Control), "15", and "30" and with your initials or group designation. The Experiment The PCR reaction pellet contains Taq DNA polymerase, the four deoxytriphosphates, Mg +2 and buffer. Sample volumes are very small. For liquid samples, it is important to quick spin the tube contents in a microcentrifuge to obtain suffi cient volume for pipeting. Spin samples for 10-20 seconds at maximum speed. CONTROL REACTION : 2. To tube "0" (Control), add the following: 2 µl DNA Template for Amplification 2 µl Primer Mix 5 µl 10x gel loading solution 10 µl Enzyme Grade Ultrapure Water. Place this control sample on ice for later electrophoresis. PCR REACTION: 3. Transfer the PCR Reaction Pellet to the appropriate sized tube (e.g. 0.2 ml or 0.5 ml) for your thermal cycler. 4. Label the tube containing the PCR Reaction Pellet as "PCR" and with your initials or group number. 5. Tap the PCR reaction tube to assure that the PCR reaction pellet is at the bottom of the tube. Add the following to the PCR tube: B Primer Mix (two primers) 10 µl D Enzyme Grade Ultrapure Water 7 µl E DNA Template for Amplification 10 µl 6. Gently mix the reaction tube. Quickly spin the PCR tube in a microcentrifuge to collect all the sample at the bottom of the tube. 7. If your thermal cycler is equipped with a heated lid, proceed directly to polymerase chain reaction cycling. If your thermal cycler does not have a heated lid, add one wax bead to the tube before proceeding to polymerase chain reaction cycling. POLYMERASE CHAIN REACTION CYCLING 8. Program the thermal cycler for a total of 30 cycles. Each cycle will be: 94 C for 45 seconds 45 C for 45 seconds 72 C for 45 seconds On the final cycle, the 72 C incubation can be extended to 5 minutes. 9. Sequentially remove samples according to the following schedule. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 11 Module I - Option A: PCR Reaction Using a Thermal Cycler, continued This experiment can also be modifi ed to remove samples at 5 cycle intervals (5, 10, 15, 20, 25 and 30 cycles). Stop After Cycle Elapsed Time Add to Tube labeled 15 45 minutes "15" 30 90 minutes "30" 10. After the 15th cycle, remove 7 µl of the PCR mixture and transfer the sample to the tube you earlier labeled "15". NOTE: If you have added wax to your reaction sample: Allow the wax to solidify (place tube on ice for a few seconds). Use a clean pipet tip to gently break through the solidifi ed wax; make enough room to fi t a clean pipet tip. Do not push the tip all the way through the solution. Discard the tip. Use a clean pipet tip to carefully remove 7 μl of the PCR mix. 11. Add 5 µl of 10x Gel Loading solution and 8 µl of Enzyme Grade Water to the 7 µl sample in the tube labeled "15". Store on ice until ready for electrophoresis. The Experiment 12. Return the PCR tube to the thermal cycler and continue the PCR reaction to the 30th cycle. NOTE: If your thermal cycler has the capability, you can to link to a program to hold samples at 4 C overnight after completing the 30th cycle. 13. After the 30th cycle, remove 7 µl of the PCR mixture and transfer the sample to the tube you earlier labeled "30". 14. Add 5 µl of 10x Gel Loading solution and 8 µl of Enzyme Grade Water to the 7 µl sample in the tube labeled "30". Store on ice until ready for electrophoresis. 15. Proceed to instructions for preparing a 0.8% agarose gel (7 x 14 cm) and separating the PCR products by electrophoresis. OPTIONAL STOPPING POINT The samples can be held in the thermal cycler at 4 C or frozen after addition of 5 μl of 10x Gel Loading Solution until ready for electrophoresis. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

12 PCR Amplification of DNA Module I - Option B: PCR Reaction Using Three Waterbaths This experiment can be adapted to use three waterbaths with heat settings at 94 C, 45 C and 72 C The Experiment Note: Superior results are obtained with a thermal cycler. Much more care needs to be taken when using the three waterbath system. The PCR incubation sample is small and can easily be evaporated. Results using three waterbaths are often variable and cannot be guaranteed. 1. Label three 0.5 ml tubes: "0" (Control), "15", and "30" and with your initials or group designation. CONTROL REACTION: 2. To tube "0" (Control), add the following: 2 µl DNA Template for Amplification 2 µl Primer Mix 5 µl 10x gel loading solution 10 µl Enzyme Grade Ultrapure Water. Place this control sample on ice for later electrophoresis. PCR REACTION: 3. Label the tube containing the PCR Reaction Pellet as "PCR" and with your initials or group number. 4. Tap the reaction tube to assure the reaction pellet is at the bottom of the tube. Add the following to the PCR tube: B Primer Mix (two primers) 10 µl D Enzyme Grade Ultrapure Water 7 µl E DNA Template for Amplification 10 µl 5. Gently mix the reaction tube. Quickly spin the PCR tube in a microcentrifuge to collect all the sample at the bottom of the tube. 6. Use clean forceps to transfer one wax bead to your "PCR" tube. At the start of the PCR reaction, the wax will melt and overlay the samples to prevent evaporation during heating. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 13 Module I - Option B: PCR Reaction Using Three Waterbaths, continued POLYMERASE CHAIN REACTION CYCLING For each cycle: Carefully place the PCR tube in a waterbath fl oat. Make sure that the sample volume is at the bottom of the tube and remains undisturbed. If a tube falls on the lab bench or fl oor, pulse spin the tube in a balanced microcentrifuge, or shake the tube to get all of the sample to the bottom of the tube. Use forceps to carefully lower the waterbath fl oat (with tubes) sequentially into the 94 C, 45 C and 72 C waterbaths for 1 minute each. 7. Cycle the PCR tube by putting it in a float and carefully transfer it back and forth between three waterbaths. Each cycle should be: 94 C for 1 minute 45 C for 1 minute 72 C for 1 minute Temperatures must be accurately maintained. 8. After the 15th cycle, transfer your tube to a rack on your lab bench to prepare the PCR sample: Place the PCR tube in the 94 C waterbath long enough to melt the wax overlay. Use a clean pipet to remove most of the melted wax overlay. Allow a thin layer of wax to solidify. Use a clean pipet tip to gently poke a hole through the solidified wax. Remove the tip. Use another clean pipet tip to enter the hole to remove 7 µl of mixture and transfer it to the tube you earlier labeled "15". Add 5 µl of 10x Gel Loading solution and 8 µl of Enzyme Grade Ultrapure Water to the 7 µl sample and store on ice. The Experiment 9. Add another wax bead to the tube and continue the reaction by transfering the PCR tube between the three waterbaths to the 30th cycle. On the final cycle the 72 C incubation can be extended to 5 minutes. 10. After the 30th cycle, transfer your tube to a rack on your lab bench to transfer and prepare a PCR sample in the tube you earlier labeled "30". Follow the procedures outlined previously in step 8. 11. The PCR amplified DNA and control samples are ready for electrophoresis. Proceed to Module II, Separating PCR Reactions by Electrophoresis. OPTIONAL STOPPING POINT The samples can be held in the thermal cycler at 4 C or frozen after addition of 5 µl of 10x Gel Loading Solution until ready for electrophoresis. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

14 PCR Amplification of DNA Module II: Separation of PCR Reactions by Agarose Gel Electrophoresis The Experiment If you are unfamiliar with agarose gel preparation and electrophoresis, detailed instructions and helpful resources are available at www.edvotek.com AGAROSE GEL REQUIREMENTS Recommended gel size: 7 x 7 cm Placement of well-former template: first set of notches Agarose gel concentration: 0.8% PREPARING THE AGAROSE GEL 1. Close off the open ends of a clean and dry gel bed (casting tray) by using rubber dams or tape. 2. Place a well-former template (comb) in the first set of notches at the end of the bed. Make sure the comb sits firmly and evenly across the bed. 3. To a 250 ml flask or beaker, add agarose powder and buffer as indicated in the Reference Tables (Appendix A) provided by your instructor. Swirl the mixture to disperse clumps of agarose powder. Important Note Continue heating until the fi nal solution appears clear (like water) without any undissolved particles. Check the solution carefully. If you see "crystal" particles, the agarose is not completely dissolved. 4. With a marking pen, indicate the level of the solution volume on the outside of the flask. 5. Heat the mixture using a microwave oven or burner to dissolve the agarose powder. 6. Cool the agarose solution to 60 C with careful swirling to promote even dissipation of heat. If detectable evaporation has occurred, add distilled water to bring the solution up to the original volume marked in step 4. After the gel is cooled to 60 C: 7. Place the bed on a level surface and pour the cooled agarose solution into the bed. 8. Allow the gel to completely solidify. It will become firm and cool to the touch after approximately 20 minutes. 9. After the gel is solidified, be careful not to damage or tear the wells while removing the rubber dams or tape and comb(s) from the gel bed. 10. Place the gel (on its bed) into the electrophoresis chamber, properly oriented, centered and level on the platform. 11. Fill the electrophoresis apparatus chamber with the appropriate amount of diluted (1x) electrophoresis buffer (refer to Table B on the instruction Appendix provided by your instructor). Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 15 Module II: Separation of PCR Reactions by Agarose Gel Electrophoresis This experiment requires a 0.8% agarose gel and is designed for staining with InstaStain Ethidium Bromide. LOADING DNA SAMPLES Reminder: Before loading the samples, make sure the gel is properly oriented in the apparatus chamber. Black Sample wells + Red 1. (Optional Step) Heat the DNA Standard marker and PCR samples for two minutes at 50 C. Allow the samples to cool for a few minutes. 2. Make sure the gel is completely submerged under buffer before loading the samples. Load 20 µl each of the samples in the following sequence: Lane Tube 1 Marker Standard DNA Fragments 2 0 Control reaction sample, 0 cycle 3 15 Reaction sample after 15 cycles 4 30 Reaction sample after 30 cycles The Experiment 3. Record the position of your sample in the gel for easy identification after staining. RUNNING THE GEL 4. After the DNA samples are loaded, properly orient the cover and carefully snap it onto the electrode terminals. 5. Insert the plugs of the black and red leads into the corresponding inputs of the power source. 6. Set the power source at the required voltage and conduct electrophoresis for the length of time determined by your instructor. 7. Check to see that current is flowing properly - you should see bubbles forming on the two platinum electrodes. 8. After the electrophoresis is completed, disconnect the power and remove the gel from the bed for staining. STAINING AND VISUALIZATION OF DNA After electrophoresis, agarose gels require staining to visualize the separated DNA samples. Your instructor will provide instructions for DNA staining with InstaStain Ethidium Bromide. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

16 PCR Amplification of DNA Module III: Size Determination of PCR Amplified DNA Fragment The size of the PCR amplified DNA fragment can be extrapolated by its migration distance relative to the Standard DNA Fragments, for which the size of each fragment is known. The Experiment Log base pairs Example fi gure 10 9 8 7 6 5 4 3 2 1 9 8 7 6 5 4 3 2 1 9 8 7 6 5 4 10,000 base pairs 1,000 base pairs 1. Measure and record the distance traveled in the agarose gel by each Standard DNA fragment (except the largest 23,130 bp fragment, which will not fit in a straight line in step 4). Plots of migration distance of marker fragments on non-logarithmic x-axis versus its size, in base pairs, on the logarithmic y-axis In each case, measure from the lower edge of the sample well to the lower end of each band. Record the distance traveled in centimeters (to the nearest millimeter). 2. Label the semi-log graph paper: A. Label the non-logarithmic horizontal x- axis "Migration Distance" in centimeters at equal intervals. B. Label the logarithmic vertical y-axis "Log base pairs". Choose your scales so that the data points are well spread out. Assume the first cycle on the y-axis represents 100-1,000 base pairs and the second cycle represents 1,000-10,000 base pairs. 3. For each Standard DNA fragment, plot the measured migration distance on the x-axis versus its size in base pairs, on the y-axis. 1 3 2 1 cm 2 cm 3 cm 4 cm 5 cm Migration Distance Quick Reference: Standard DNA fragment sizes - length is expressed in base pairs. 23130 9416 6557 4361 3000 2322 2027 725 570 4. Draw the best average straight line through all the points. The line should have approximately equal numbers of points scattered on each side of the line. Some points may be right on the line (see Example figure at left). 5. Using the graph of the Standard DNA fragments, determine the sizes in base pairs of the main PCR amplified DNA from this curve. A. Find the migration distance of the PCR amplified DNA on the x-axis. Draw a vertical line from that point until the standard graph line is intersected. B. From the point of intersection, draw a second line horizontally to the y-axis and determine the approximate size of the PCR amplified DNA in base pairs (refer to Figure example). Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 17 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 Y-axis: Log Base Pairs 2,000 1,000 900 800 700 600 500 400 300 200 The Experiment 100 90 80 70 60 50 40 30 20 Duplication 10 of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706 1 cm 2 cm 3 cm 4 cm 5 cm 6 cm X-axis: Migration distance (cm)

18 PCR Amplification of DNA Study Questions Answer the following study questions in your laboratory notebook or on a separate worksheet. 1. Why is a thermostable DNA polymerase required for PCR-based DNA amplification? The Experiment 3. How many copies of the DNA to be amplified is achieved after 4 and 8 cycles? 3. Why are two different primers required for the PCR reaction? 4. What are possible reasons for obtaining fainter (usually smaller) bands besides the main PCR product? Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 19 Instructor s Guide Class size, length of laboratory sessions, and availability of equipment are factors which must be considered in the planning and the implementation of this experiment with your students. These guidelines can be adapted to fit your specific set of circumstances. If you do not find the answers to your questions in this section, a variety of resources are continuously being added to the EDVOTEK web site. In addition, Technical Service is available from 9:00 am to 6:00 pm, Eastern time zone. Call for help from our knowledgeable technical staff at 1-800-EDVOTEK (1-800-338-6835). NATIONAL CONTENT AND SKILL STANDARDS By performing this experiment, students will learn to load samples and run agarose gel electrophoresis. Analysis of the experiments will provide students the means to transform an abstract concept into a concrete explanation. Please visit our website for specific content and skill standards for various experiments. EDVO-TECH SERVICE 1-800-EDVOTEK Mon - Fri (1-800-338-6835) 9 am - 6 pm ET Technical Service Department Mon - Fri 9:00 am to 6:00 pm ET FAX: 202-370-1501 Web: www.edvotek.com email: info@edvotek.com Please have the following information ready: Experiment number and title Kit lot number on box or tube Literature version number (in lower right corner) Approximate purchase date EDUCATIONAL RESOURCES Electrophoresis Hints, Help and Frequently Asked Questions EDVOTEK experiments are easy to perform and designed for maximum success in the classroom setting. However, even the most experienced students and teachers occasionally encounter experimental problems or difficulties. The ED- VOTEK web site provides several suggestions and reminders for conducting electrophoresis, as well as answers to frequently asked electrophoresis questions. Online Ordering now available Visit our web site for information about EDVOTEK s complete line of hands-on experiments for biotechnology and biology education. EDVOTEK - The Biotechnology Education Company 1-800-EDVOTEK www.edvotek.com FAX: 202-370-1501 email: info@edvotek.com EVT.120706

20 PCR Amplification of DNA Notes to the Instructor: MAXIMIZING PCR EXPERIMENTAL SUCCESS Please refer to the Appendices for a summary of important hints and reminders to help maximize successful implementation of this experiment. This experiment has three modules: The Experiment I. PCR Reaction II. Separation of PCR Reactions by Electrophoresis III. Size Determination of PCR Amplified DNA Fragment There are two options for performing the PCR reactions. The preferred option is A, which requires a thermal cycler. Option B adapts this experiment to utilize three water baths at 94 C, 45 C and 72 C. It should be emphasized that superior results are obtained with a thermal cycler. Much more care needs to be taken when using the water bath system since PCR incubation sample is small and can easily be evaporated. Results using waterbaths will vary and cannot be guaranteed. MICROPIPETTING BASICS AND PRACTICE GEL LOADING Accurate pipeting is critical for maximizing successful experiment results. EDVOTEK Series 300 experiments are designed for students who have had previous experience with agarose gel electrophoresis and micropipeting techniques. If your students are unfamiliar with using micropipets, EDVOTEK highly recommends that students perform Experiment # S-44, Micropipetting Basics, or other Series 100 or 200 electrophoresis experiment prior to conducting this advanced level experiment. APPROXIMATE TIME REQUIREMENTS 1. The PCR step (15 and 30 cycles) will take approximately 45 and 90 minutes respectively for Option A, which uses a Thermal Cycler. Option B, which uses three waterbaths, will take longer. 2. The experiment can be temporarily stopped after the completion of Module I (PCR Reaction) and later resumed. Experimental results will not be compromised if instructions are followed as noted under the heading Optional Stopping Point at the end of Module I. 3. Whether you choose to prepare the gel(s) in advance or have the students prepare their own, allow approximately 30-40 minutes for this procedure. Generally, 20 minutes of this time is required for gel solidification. See section Options for Preparing Agarose Gels which follows. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 21 Notes to the Instructor: Table C Volts 125 70 50 Time and Voltage Recommendations EDVOTEK Electrophoresis Model M6+ M12 & M36 Minimum / Maximum Minimum / Maximum 20 / 30 min 35 / 45 min 50 / 80 min 35 / 45 min 60 / 90 min 95 / 130 min 4. The approximate time for electrophoresis will vary from 20 minutes to 2 hours. Generally, the higher the voltage applied, the faster the samples migrate. However, depending upon the apparatus configuration and the distance between the two electrodes, individual electrophoresis units will separate DNA at different rates. Follow manufacturer's recommendations. Time and Voltage recommendations for EDVOTEK equipment are outlined in Table C. OPTIONS FOR PREPARING AGAROSE GELS This experiment is designed for DNA staining after electrophoresis with InstaStain Ethidium Bromide. Students will share gels in this experiment. Each 0.8% gel should be loaded with the Standard DNA markers and samples from 4 or 5 students. The control PCR reaction can also be loaded in one of the wells. Instructor s Guide There are several options for preparing agarose gels for the experiment. 1. Individual Gel Casting: Each student lab group can be responsible for casting their own individual gel prior to conducting the experiment. 2. Preparing Gels in Advance: Gels may be prepared ahead and stored for later use. Solidified gels can be stored under buffer in the refrigerator for up to 2 weeks. Do not store gels at -20 C. Freezing will destroy the gels. Gels that have been removed from their trays for storage, should be "anchored" back to the tray with a few drops of hot, molten agarose before placing the gels into the apparatus for electrophoresis. This will prevent the gels from sliding around in the trays and the chambers. 3. Batch Gel Preparation: A batch of agarose gel can be prepared for sharing by the class. To save time, a larger quantity of UltraSpec-Agarose can be prepared for sharing by the class. See instructions for "Batch Gel Preparation". GEL CONCENTRATION AND VOLUME The gel concentration required for this experiment is 0.8%. Prepare gels according to Table A.1 or A.2 in Appendix D. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

22 PCR Amplification of DNA Notes to the Instructor: GEL STAINING AND DESTAINING AFTER ELECTROPHORESIS Instructor s Guide After electrophoresis, the agarose gels require staining in order to visualize the separated DNA samples. This experiment features a proprietary stain called InstaStain. InstaStain EtBr (Appendix F) Optimal visualization of PCR products on gels is obtained by staining with InstaStain Ethidium Bromide (InstaStain EtBr) cards. Exercise caution when using Ethidium Bromide, which is a listed mutagen. Disposal of the InstaStain EtBr cards, which contain only a few micrograms of ethidium bromide, is minimal compared to the large volume of liquid waste generated by traditional ethidium bromide staining procedures. Disposal of InstaStain cards and gels should follow institutional guidelines for chemical waste. InstaStain Blue: One-step Staining and Destaining (Appendix G) InstaStain Blue can be used as an alternative for staining gels in this experiment. However, InstaStain Blue is less sensitive than InstaStain EtBr and will yield variable results. Agarose gels can be stained and destained in one easy step, which can be completed in approximately 3 hours, or can be left in liquid overnight. For the best photographic results, leave the gel in liquid overnight. This will allow the stained gel to "equilibrate" in the destaining solution, resulting in dark blue DNA bands contrasting against a uniformly light blue background. Gels stained with InstaStain Blue may be stored in the refrigerator for several weeks. Place the gel in a sealable plastic bag with destaining liquid. DO NOT FREEZE AGAROSE GELS! Used InstaStain Blue cards and destained gels can be discarded in solid waste disposal. Destaining solutions can be disposed down the drain. PHOTODOCUMENTATION OF DNA (OPTIONAL) There are many different photodocumentation systems available, including digital systems that are interfaced directly with computers. Specific instructions will vary depending upon the type of photodocumentation system you are using. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

PCR Amplification of DNA 23 Pre-Lab Preparations MODULE I - PCR REACTION 1. Program the thermal cycler or equilibrate waterbaths. Each Group Requires: A One (1) PCR Reaction Pellet (in tube) PCR pellet contains: dntp Mixture, Taq DNA Polymerase Buffer, Taq DNA Polymerase & MgCl 2 B Primer Mix 12 µl D Enzyme Grade Ultrapure Water 30 µl E DNA Template for Amplification 12 µl 10x Gel Load 25 µl *Wax bead (use only if required) 2 If performing Option A, program the thermal cycler for the following setup for 30 cycles: 94 C 45 seconds 45 C 45 seconds 72 C 45 seconds (5 minutes for the end of the final cycle) If performing Option B, equilibrate one waterbath at 94 C, a second waterbath at 45 C, and a third waterbath at 72 C. 2. Place the DNA Template for Amplification (E) and the Primer Mix (B) on ice. 3. Aliquot the amounts of reagents indicated in the box at left to each tube using a fresh pipet tip for each component. Alternatively, you can set up a pipeting station for the class. MODULE II: ELECTROPHORESIS 4. Aliquot 20 µl of the Standard DNA markers (C) into microcentrifuge tubes. Distribute one tube of markers per gel. Instructor s Guide Notes and Reminders: Accurate temperatures and cycle times are critical for PCR. A pre-run for one cycle (approx. 3 to 5 minutes) is recommended to check that the thermal cycler is properly programmed. For thermal cyclers that do not have a top heating plate, it is necessary to place a layer of wax above the PCR reactions in the microcentrifuge tubes to prevent evaporation. See Appendix entitled Preparation and Handling PCR Samples with Wax. Three water baths can be used for PCR if a thermal cycler is unavailable. The experiment will require great care and patience. Samples will require wax layers. See appendices entitled Polymerase Chain Reaction Using Three Waterbaths and Handling samples with wax overlays. Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

24 PCR Amplification of DNA Experiment Results and Analysis Instructor s Guide The idealized schematic shows the approximate intensity of the PCR amplifi ed band after various cycles. Actual results will yield broader bands of varying intensities in the Standard DNA Fragments (Lane 1). Smaller fragments will stain less effi ciently and will appear as fainter bands. The idealized schematic shows the relative positions of the bands, but are not depicted to scale. Lane 1 Standard DNA fragments Lane 2 Control reaction sample after 0 cycles Lane 3 Reaction sample after 15 cycles Lane 4 Reaction sample after 30 cycles 23130 bp 9416 bp 6557 bp 4361 bp 3000 bp 2322 bp 2027 bp 725 bp 570 bp ( - ) 1 2 3 4 5 6 ( + ) Idealized Schematic - 7 x 7 cm gel In some experiments, a faint band above the PCR amplified DNA band may also be visible (not shown in idealized schematic), which is the DNA template. The predominant band is the PCR product. Likewise, smaller bands may be faintly visible at the bottom of the gel due to partial PCR amplifcation products or primer. Photo Example of PCR amplifi ed DNA NOTE: Because waterbaths do not maintain temperatures as precisely as a thermal cycler, additional faint template artifact bands may possibly be observed in the control and PCR lanes in some experiments. Lanes 2-6 represent amplifi ed DNA obtained after 0, 5, 10, 15 and 20 cycles respectively Duplication of any part of this document is permitted for non-profi t educational purposes only. Copyright 1996-2012 EDVOTEK, Inc., all rights reserved. EVT.120706

Please refer to the kit insert for the Answers to Study Questions

26 xxx PCR Amplification of DNA EVT.120706 EDVOTEK -

PCR Amplification of DNA 27 Appendices A B C D E F G PCR Experimental Success Guidelines Polymerase Chain Reaction Using Three Waterbaths Preparation and Handling of PCR Samples With Wax 0.8% Agarose Gel Preparation 0.8% Agarose Gels - Quantity Preparations Staining and Visualization of DNA with InstaStain Ethidium Bromide Cards InstaStain Blue: One Step Staining and Destaining Material Safety Data Sheets EDVOTEK - The Biotechnology Education Company 1-800-EDVOTEK www.edvotek.com FAX: 202-370-1501 email: info@edvotek.com EVT.120706

28 Appendix A PCR Experimental Success Guidelines EDVOTEK experiments which involve the amplification of DNA are extremely relevant, exciting and stimulating classroom laboratory activities. These experiments have been performed successfully in many classrooms across the country, but do require careful execution because of the small volumes used. The following guidelines offer some important suggestions, reminders and hints for maximizing success. THE PCR REACTION 1. Add Primers and DNA to the PCR Reaction Bead: Add the primer mixture (forward and reverse primers) and the cell DNA (supernatant) as specified in the experimental procedures to the microcentrifuge tube containing the PCR reaction bead. Make sure that the bead (which contains the Taq DNA polymerase, the 4XdTPs, Mg and the PCR reaction buffer) is completely dissolved. Do a quick spin in a microcentrifuge to bring the entire sample to the bottom of the tube. Prepare the control reaction similarly. 2. The Thermal cycler: It is critical that the thermal cycler be accurately programmed for the correct cycle sequence, temperatures and the time for each of the cycles. 3. Oil or Wax: For thermal cyclers that do not have a top heating plate, the reaction in the tubes must be overlaid with oil or wax to prevent evaporation. 4. Manual Water Bath PCR: Three water baths can be used as an alternative to a thermal cycler for PCR, but results are more variable. Samples require oil or wax layers. This method requires extra care and patience. GEL PREPARATION AND STAINING 5. Concentrated agarose: Gels require special attention when dissolving or re-melting. Make sure that the solution is completely clear of clumps or glassy granules. Distorted electrophoresis DNA band patterns will result if the gel is not properly prepared. 6. Electrophoretic separation: The tracking dye should travel at least 4 cm from the wells for adequate separation before staining. 7. Staining: Staining of gels require care to obtain clear, visible results. After staining (15 to 30 min.) with InstaStain Ethidium Bromide or liquid ethidium bromide, examine the results using a UV (300 nm) transilluminator. Repeat the staining as required. Gels stained with InstaStain Blue or liquid Blue stain may fade with time. Restain the gel to visualize the DNA bands. 8. Standard DNA Markers: After staining the agarose gel, the Standard DNA markers should be visible. If bands are visible in the markers and control lanes, but bands in the sample lanes are faint or absent, it is possible that DNA was not successfully extracted from the cells. If the marker, control and DNA bands are all faint or absent, potential problems could include improper gel preparation, absence of buffer in the gel, improper gel staining or a dysfunctional electrophoresis unit or power source. Duplication of this document, in conjunction with use of accompanying reagents, is permitted for classroom/laboratory use only. This document, or any part, may not be reproduced or distributed for any other purpose without the written consent of EDVOTEK, Inc. Copyright 1996, 1997, 1998, 1999, 2000, 2001, 2005, 2007, 2008, 2009, 2011 EDVOTEK, Inc., all rights reserved. EVT.120706

Appendix B Polymerase Chain Reaction Using Three Waterbaths 29 Superior PCR results are obtained using an automated thermal cycler. However, if you do not have a thermal cycler, this experiment can be adapted to use three waterbaths (Cat. # 544). Much more care needs to be taken when using the three-waterbath PCR method. The PCR incubation sample is small and can easily be evaporated. Results using three waterbaths are often variable. Please refer to the Appendix entitled "PCR Samples with Wax Overlays" for sample handling and preparation tips. Each PCR Reaction pellet contains Taq DNA polymerase, four deoxytriphosphates, Mg +2 and buffer. PREPARATION OF THE PCR REACTION: 1. The PCR reaction sample should be prepared as specified in the experiment instructions. Each PCR reaction sample contains three critical components: PCR Reaction pellet Primer mix DNA for amplification 2. After adding the components of the PCR reaction sample, use clean forceps to transfer one wax bead to the PCR tube. At the start of the PCR reaction, the wax will melt and overlay the samples to prevent evaporation during heating. POLYMERASE CHAIN REACTION CYCLING Important Note It is imperative that the temperatures are accurately maintained throughout the experiment. 3. In the three-waterbath PCR method, the PCR reaction sample is sequentially cycled between three separate waterbaths, each set at different temperatures, for a specified period of time. The sequential placement of the reaction sample in the waterbaths maintained at three different temperatures constitutes one PCR cycle. One example of a PCR cycle might be as follows: 94 C for 1 minute 50 C for 1 minute 72 C for 1 minute See experiment instructions for specific program requirements. 4. The PCR tube must be handled carefully when sequentially cycled between the three waterbaths. For each cycle: Carefully place the PCR tube in a waterbath float. Make sure that the sample volume is at the bottom of the tube and remains undisturbed. If necessary, pulse spin the tube in a balanced microcentrifuge, or shake the tube to get all of the sample to the bottom of the tube. Use forceps to carefully lower the waterbath float (with tubes) sequentially into the waterbaths. 5. Process the PCR reaction sample for the total number of cycles specified in the experiment instructions. On the final cycle the 72 C incubation can be extended to 5 minutes. 6. After all the cycles are completed, the PCR sample is prepared for electrophoresis.

30 Appendix C Preparation and Handling of PCR Samples With Wax For Thermal Cyclers without Heated Lids, or PCR Using Three Waterbaths Automated thermal cyclers with heated lids are designed to surround the entire sample tube at the appropriate temperature during PCR cycles. Heating the top of the tubes during these cycles prevents the very small sample volumes from evaporating. For thermal cyclers without heated lids, or when conducting PCR by the three-waterbath method, it is necessary to add a wax bead to the reaction sample. During the PCR process, the wax will melt and overlay the samples to prevent evaporation during heating. Each PCR Reaction pellet contains Taq DNA polymerase, four deoxytriphosphates, Mg +2 and buffer. PREPARING THE PCR REACTION: 1. The PCR reaction sample should be prepared as specified in the experiment instructions. Each PCR reaction sample contains the following three critical components: PCR Reaction pellet Primer mix DNA for amplification 2. After adding the components of the PCR reaction sample, use clean forceps to transfer one wax bead to the PCR tube. 3. Process the PCR reaction sample for the total number of cycles specified in the experiment instructions. PREPARING THE PCR REACTION FOR ELECTROPHPORESIS: 4. After the cycles are completed, transfer the PCR tube to a rack and prepare the PCR sample for electrophoresis. Place the PCR tube in a 94 C waterbath long enough to melt the wax overlay. Use a clean pipet to remove most of the melted wax overlay. Allow a thin layer of the wax to solidify. Use a clean pipet tip to gently poke a hole through the solidified wax. Remove the tip. Use another clean pipet tip to enter the hole to remove the volume of mixture specified in the experiment instructions. Transfer this volume to a clean tube. Add other reagents according to experiment instructions, if applicable,. Add 5 µl of 10x Gel Loading solution to the sample and store on ice. 5. Proceed to delivery of the sample onto an agarose gel for electrophoresis as specified in the experiment instructions. Duplication of this document, in conjunction with use of accompanying reagents, is permitted for classroom/laboratory use only. This document, or any part, may not be reproduced or distributed for any other purpose without the written consent of EDVOTEK, Inc. Copyright 1996, 1997, 1998, 1999, 2000, 2001, 2005, 2007, 2008, 2009, 2011 EDVOTEK, Inc., all rights reserved. EVT.120706